Thats pretty good logic, HOWEVER, if your fillets are some form of epoxy, or cured material, be very carefull not to allow build up of dope on the fillets as by nature dope shrinks, and can pull away from the fillet material.
I agree in principle that filler after the fillets makes sense since you can then more effectivly eliminate any edge from the fillet material, just dont build up on the fillets themselves. and dont use shrinking dope in your filler.